“The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth.”
C. Darwin
The family history…
The following is a very brief and spotty recounting of your family history. OK, our family tree.
In the beginning… there were bacteria-like single-celled blobs. This beginning is somewhere shy of 4 billion years ago. We think.
About 3 billion years ago, some of these bacteria learned to use the energy of the sun in the first photosynthesis, and produced oxygen as a byproduct. A huge amount of oxygen slowly accumulated, which was toxic to most life at the time, and eventually led to the “Great Oxidation Event” about 2.4 billion years ago. That oxygen also reacted with iron in the water, and today we find that as iron ore all around the world in places like the Mesabi Range in Minnesota.
Some bacteria learned to use that excess oxygen. Soon after, cells appeared with nuclei (called eukaryotes) most likely by bacteria-like cells (called prokaryotes, which have no nucleus) engulfing each other and becoming symbiotic. Importantly, a bacterial cell which could generate energy from oxygen was engulfed by a cell which could not use oxygen, and the two learned to cooperate to each other’s benefit. The oxygen-using bacteria became mitochondria, the power plants within our cells. This was about 1.85 billion years ago.
The first multi-cellular plants may have moved onto land about a billion years ago.
The first multi-cellular animals arose somewhere between 580-542 million years ago. But these first animals were still pretty blobby. The first simple structured animals like today’s sponges and corals and sea anemones arose about 550 million years ago.
Something called the Cambrian explosion occurred about half a billion years ago, and this is where the basic body plan of all the animals we know today first arose – by body plan I mean animals with a front and back and mirror-imaged left and right sides (like flat worms), with segments and a gut (like segmented worms), animals with exoskeletons (like insects, crabs, spiders), or vertebrae and a spinal cord (like hagfish), a skull and jaws (like bony fish), etc. These and many others arose during the Cambrian explosion. But all these primordial animals still lived only in water.
The first footprints on land were about 530 million years ago… but the creatures leaving those tracks were arthropods, and not directly related to us. They were more like distant cousins, so we’ll leave that branch of the family history there.
We still need to remain in the water for quite a while longer for our direct family tree… and those are the first vertebrates or jawless fish which arose from simpler invertebrates (probably a worm-like animal) about 485 million years ago. Those jawless fish gave rise to the first jawed vertebrate fish perhaps around 443 million years ago.
A major change occurred when fish learned to come ashore and gave rise to the first amphibian about 365-395 million years ago (the latter time is when the first four-legged animal tracks are found on land).
The next major evolutionary change was the rise of the first reptiles about 330 million years ago… where their innovation was the ability to lay eggs on land. That was a real game-changer because now this is the first time that animals were able to live their entire lives on land (remember that amphibians lay eggs and start their lives in water).
A branch of reptiles became warm-blooded, evolved hair, and eventually gave rise to the first mammals maybe about 200 million years ago. But the early mammals were probably small, scurrying, nocturnal, ground-dwelling critters and were dominated by another branch of reptile descendants, the dinosaurs, who ruled many of the ecological niches on land, sea and air.
When an asteroid punched a hole in the earth in what is now the Gulf of Mexico about 66 million years ago, the dinosaurs were wiped out and this gave room for mammals – and eventually us – to take over the niches left empty by their extinction (one of several mass extinctions that punctuated and shaped the story of life on Earth, like the way The Black Death punctuated and shaped the history of humans in Eurasia).
Darwin’s tree of life…
You probably know that the family history we just recounted in such a rushed and human-centric way is based on a Darwinian understanding of evolution, the generation of new species by variation and natural selection.
Over 150 years ago Darwin recognized our evolutionary relatedness in his book On the Origin of Species, that we and all life arose from a universal common ancestor:
"Therefore, on the principle of natural selection with divergence of character, it does not seem incredible that, from some such low and intermediate form, both animals and plants may have been developed; and, if we admit this, we must likewise admit that all the organic beings which have ever lived on this earth may be descended from some one primordial form."
Darwin marshalled an enormous range of data and observations to support his theory. But one of the important bits of data was the common skeletal pattern of similar structures like limb bones:
“We never find, for instance, the bones of the arm and forearm, or of the thigh and leg, transposed. Hence the same names can be given to the homologous bones in widely different animals.”
“What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?”
A more specific and powerfully predictive formulation of Darwin’s theory says that organisms with shared features (called homologous) means they shared a common ancestor. For example, the limbs in humans, whales, lizards, and birds are homologous, because these diverse species must have come from a simpler ancestral organism which had limbs, and which gave rise to all the species today with limbs:
“If we suppose that an early progenitor—the archetype, as it may be called—of all mammals, birds and reptiles, had its limbs constructed on the existing general pattern, for whatever purpose they served, we can at once perceive the plain signification of the homologous construction of the limbs throughout the class.”
“…in regard to the members of each great kingdom, such as the Vertebrata, Articulata, etc., we have distinct evidence in their embryological, homologous, and rudimentary structures, that within each kingdom all the members are descended from a single progenitor.”
We have a single upper limb bone (humerus in the arm or femur in the leg), attached to two lower limb bones (radius and ulna in the arm), connected to a bunch of bones in the wrist (carpals), and finally the digits (phalanges) at the very end of the limb… and that pattern is carried all the way across all of the tetrapods (four-limbed animals including amphibians, reptiles, birds, and mammals) from today all the way to the earliest amphibian in the fossil record over 365 million years ago.
Skeletons in the closet…
That family resemblance of limb bones among such a diverse range of animals, from humans and mammals to birds and reptiles to amphibians, comes to a screeching halt at the next earlier group of animals in that evolutionary sequence – fish.
We are certain from the fossil record that fish gave rise to amphibians, firstly because we see that fish fossils predate amphibian fossils. But also, using that Darwinian framework of homology, we conclude that there is nothing else which could be ancestral to animals like salamanders and frogs. Plants cannot have directly given rise to amphibians, nor can insects, or mollusks, or sea urchins, or corals. Fish, however, share essential homologous characteristics with amphibians that those other types of animals do not. For example, fish and amphibians both have a vertebral column and a spinal cord. They have a skull with a toothy jaw and encasing a brain. They have a bilateral body plan, etc. Therefore, Darwin’s theory predicts that some ancient fish were ancestral to today’s amphibians and fish.
But… Fish have fins. Not arms and legs.
One of many puzzles in our understanding of how evolution played out in our past is: how did that evolutionary transformation from fins to limbs happen?
This is one of many question that has perplexed evolutionary biologists since Darwin’s days. We have had many fossil fish and many fossil amphibians to examine over the past couple centuries. But for the longest time we had nothing to show how the transition from fin to foot happened.
Enter Jennifer Clack, Ph.D.
Clack was born in Manchester, U.K. in 1947, and like many kids showed a fascination with fossils. But unlike most kids, Clack’s fascination did not waver and fade with age and maturity. In 1970 Clack earned a degree in zoology from the University of Newcastle upon Tyne. In her final year there, she took a class with Alec Panchen who was studying Carboniferous tetrapod fossils. It was not until 1978 that Clack was finally able to begin her Ph.D. with Panchen, where she studied the ear bones of a Carboniferous amphibian called Pholiderpeton (Carboniferous refers to a large chunk of time from about 359 to 399 million years ago). In 1980 she married a fellow motorcyclist and music and fossil enthusiast, Rob Clack. Starting in 1981, Clack found her lifetime home at the University Museum of Zoology in Cambridge, U.K., where she rose from Assistant Curator to Emeritus Professor of Vertebrate Paleontology over a four-decade career.
In 1986, in the Sedgewick Museum in Cambridge, Clack stumbled on some fossils from the Late Devonian (419-359 million years ago), collected in the 1960s from eastern Greenland and since forgotten. She recognized them as early amphibians. At that time, there were only three Devonian tetrapods known, and two of them were from eastern Greenland: Acanthostega and Icthyostega. Icthyostega fossils were numerous and fairly complete, but Acanthostega was mostly a name given to a fragment of a skull. What Clack had found in Sedgewick were Acanthostega skulls with a bit of vertebra. These ancient amphibians likely lived near the time when animals first made their way onto land. She was hooked. Clack recognized that more complete fossils of these animals might be able to answer long-standing questions on the evolution from fish to amphibians, and this accidental find of a few fossil bones in some museum closet made her career.
Clack organized her first expedition to Greenland in June, 1987 with her husband Rob, her first Ph.D. student Per Ahlberg, two colleagues from Denmark, and the original 1960’s field notes. Six weeks of quarrying among the Devonian deposits of Greenland yielded the largest cache of tetrapods recovered in a single season including the elusive Acanthostega.
But the really hard work had just begun on her return from the field. After many years of work by Clack and her team preparing and analyzing the fossils, Acanthostega is now the most completely described Devonian amphibian or early tetrapod. Among other things her lab showed that these animals retained fish-like internal gills, and had eight toes and seven fingers, rather than the expected five digits per limb. The limbs were paddle-like and were not shaped well for weight-bearing and suggested an aquatic life, consistent with an amphibian that was early in the transition to land.
Clack’s work was the first to significantly raise the curtain on the evolution of limbs, and to push our detailed knowledge of our own family tree back further in time and closer to our fish ancestors.
But there was more work to do to fill in the gaps.
A fish with hands …
A look at the most advanced limb-like bones in fish fossils at the time (Eusthenopteron and Pandericthys) shows a big jump between the lobed fin of a fish, to the clearly limb-like paddle of the early amphibian Acanthostega. There had to be something between which shows how the fin transitioned to a structure with one upper limb bone, two lower limb bones, many small wrist bones, and five (or more) digits at the very ends.
An anatomist and paleontologist at the University of Chicago named Neil Shubin aimed to fill in the gaps. He knew the time period in which the fish most closely related to amphibians lived (Panderichthys, about 380 million years ago), and the amphibian that Clack studied which was most closely related to fish (Acanthostega, about 365 million years ago). He therefore had a narrow window of time between them in which to find fossils that might shed light on the evolution from fin to limb.
A geology textbook is credited with giving insight into the specific formation of rocks of the right age and proximity to the surface to be a good candidate for fossil hunting. Unfortunately, these rocks were in the Canadian arctic and allowed only a few weeks of prospecting per year.
After about six years of effort, Shubin’s team found a fish, Tiktaalik rosea, that lived between 380-365 million years ago – right between the periods when Pandericthys and Acanthostega thrived. Tiktaalik had scales and fins like a fish, but also had a neck and a flat head almost like an alligator. The ribs were large and connected implying the need for support outside of water. Within the fin the bones formed structures like a wrist and digits and were structured in a way to enable some weight support. But beyond the digits the fins also showed the rays or spines that we normally associate with fish fins. This clearly was a fish with hands – within a fin.
The story of this remarkable discovery is told beautifully in Neil Shubin’s popular book and TV series, Your Inner Fish.
Filling in the gaps…
But there were still gaps in the story of how the hand evolved from fish to amphibian. Literally. The bones in the digits of Tiktaalik were not complete, and the full fin model was based on best guesses to fill in the few missing bones.
This is where John A. Long, a paleontologist at Flinders University in South Australia comes in. His team (including Michael Lee who was a former graduate student of Clack, and Alice Clement who did post-doctoral research with Per Ahlberg, Clack’s very first graduate student) just published a paper showing the full pectoral fin of a fish called Elpistostege. The fin had the fin rays characteristic of fish, yet also had the familiar limb pattern of amphibians. Importantly, the fin contained bones similar to the wrist and digits of the hand.
Elipistostege was known from only a few fragmentary fossils before, but this recent find came from the Miguasha cliffs of the Gaspe Peninsula in eastern Quebec, and is one of the most complete and well-preserved fish fossils from this period.
The interesting thing is that Long’s team used computed tomography or CT scans similar to what radiologists use to get a 3-dimensional view of your anatomy, but with stronger x-rays to view the fossils embedded within rock.
This new work has given us a much clearer and complete view of the bony anatomy of this intermediate species, and a possible evolutionary step between Tiktaalik and Acanthostega that further blurs the line between fish and amphibian.
The main lesson from Tiktaalik and Elpistostege is that the basic pattern for making arms and hands appeared within fish fins long before the form or function of a limb or hand arose in the first amphibians, hands that are recognizably related to ours.
Our own little evolutionary twig…
If we go back to that family history, we can see that we are at the tail end of a long, dramatic and amazing story, that the main trunk and many branches of our family tree is thick with uncounted family members, and that we are a tiny twig at the very periphery of that huge tree.
If we look at each feature from our DNA to our brains, from our eyes and hair and limbs to the way we are shaped and made in the womb and grow through life, we see that we follow the convoluted, random, and imperfect path set by our evolutionary past. The proteins that make up the light-sensing molecules in our eyes to the proteins that program how our eyes are made, to the bones that make up our hands and vertebrae and skull, all these and more find homologies among related species near and far. These homologies occur hand-in-hand with tremendous variation (the fuel for evolution) within a given species.
This is incredibly powerful and beautiful. It is beautiful because the homologies show us how intimately related we are to everything from the hydrangeas in your garden to the worms and insects and neighbors trespassing in your flower beds. And the variations within a species show us how each of us still retains our uniqueness and individuality. It is powerful because it underlies why we can use simpler animals like flies and worms and even single celled yeast to try and understand our own biology and create new medicines and therapies.
We are still only scratching the surface of the biology that Darwin kicked off for us a century and a half ago, and his closing words in his greatest book still apply today:
“…whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”
Note: Jennifer Clack recently passed away after several years fighting cancer. She died March 26, 2020. She is survived by her husband Rob, and a museum full of her amazing fossils.
If you got this far, I thank you for reading! I know this is a long article and I appreciate you slogging though this. If you enjoyed reading this as much as I did writing it, please forward it along whether by email to family and friends, or linked on your social media. And encourage others to subscribe and read - and to contact me to yell about something they disagreed with or didn't like. The feedback is important to me. And don't forget to check out the other posts here:
This blog post was inspired by Neil Shubin's book Your Inner Fish which I read almost 10 years ago now, as well as this recent article by Richard Cloutier et al:
Jennifer Clack's article describing Acanthostega limbs is here:
Clack has a book called Gaining Ground which I have not yet read but is on the long list of books to get someday:
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